Picked up this bike over the past weekend. Its been sitting for 15 years. I pretty much immediately removed the carbs to clean them since I knew they would need it badly. I was very successful in not ruining any of the gaskets, or the fuel accell diaphram. All jet passages came completely clean.

However, some of the other passages wouldnt clear out, which I later traced to the air cutoff valves. My carb cleaner definitely ruined all 4 of the diaphrams. I removed the only one accessible while the carbs are all together. I just blocked it off completely since it was ruined. I have ordered 4 new air cut off valves.

The bike will start and run well with full choke. I can hold the choke steadily and make it idle at 1200rpms or so, but as soon as I let off full choke, it dies.

Do the air cut off valves have anything to do with the idle system?

How about the pilot valves?

It seems like air leakage could cause some of this, and when I spray starting fluid on the carbs it speeds up, but I cant figure out where any air could be getting in...

Welcome here! One very essential and recommended thing is to check and clean out your tank. There is a filter screen at the petcock inside the tank. Worth a look. Place a hose on the petcock, turn on reserve and let some fuel into a jar. Then you see whether you like to have this in your carbs. An inline filter may help, too.No idea about the air cutoff system impact on idle, this is unique to '79 models. Plugged pilot jets or very low floater levels may cause the behaviour you describe.The CB650 needs the choke for some time, however without touching the throttle, it should also stay alive at half choke after 30 seconds or so.With that air leak you probably won't get a reasonable idle behaviour, so try to identify it. Maybe cracked carb boots.Looks like your #4 mixture screw is broken in the thread or missing. The latter might cause a slight reaction on starting fluid.

Yeah I bumped the pilot screw and it broke off. Previously I cleaned the tank out and ran fuel out of it into a clean container. Do the pilot screws adjust mixture for idle? Its a poor design, since you can't adjust them past a full turn with the bowls in place! I will now have to remove the bowls to verify the proper setting. Which passage is for the slow jet? I know which one is the main. The boots coming off the sides of the carbs that tee into each other are all good with no cracks. The manual online at http://cosky0.tripod.com/ tries to show the slow jet, but the page is too dark for me to tell.

Yes, clean fuel is a good starting point. The slow jets are these shorter tubes next to the main jets. They are pressed in and due to that may look different from what you expected. Make sure they are free, some here recommend guitar strings. A single strand from a stranded copper wire will do the job, too, but don't try steel wire.In fact these finned screws are to adjust idle mixture. These stupid fins seem to be a unique US feature (maybe California only?), never seen them on my carbs. Turn out the screws, fix them in a bench vise and solve this with a file. Nevertheless you might get ahead with that fins as soon as everything else is all right. Idle screws are just fine tuning and won't compensate any serious fault issues like e.g. air leaks or blocked jets.With carb boots I meant the short, thick-walled rubber hoses that mount the carbs to the engine intake ports. I think the parts you refer to are what we usually call (vacuum) tees here in this forum. Nevertheless it is good to have them all right.

I cleaned out the slow jets, and installed new air cut off diaphrams. The bike pretty much idles fine now, but it doesnt respond well during acceleration. It idles fine with no choke at all, but then as soon as you hit the throttle it will want to die. If I choke it half way as im giving it throttle it acts normal and has lots of power. Acts like its getting too much air. I dont know if this would account for all of it, but i dont have any air restriction from air filter/housing. For temporary i only have the carbs on, with nothing before them on the intake side. Also after i've been riding it a bit, it wants to idle fast.

Seems to me like you progressed fixing things beyond a point where open carb tests don't make sense any more. Be sure without airbox or anything is even worse than pods. Certainly too lean, which explains the need for choke. Use the opportunity of free view to check whether your accelerator pump works (spray of fuel on throttle twist in all four carbs) and then install the airbox and air filter. This will compensate the need for air restriction by the choke and maybe it will already run fine then. Now it certainly cannot work properly with that stock jetting/open carbs configuration.